The court in the northern Jaffna peninsula ordered the release of the fishermen who were detained by the Sri Lankan Navy in mid-December in the seas south of Mannar.
"Happy to learn that a Court has ordered the release of 56 #Indian fishermen," Indian High Commission in Colombo said in a tweet.
"Commend the work of High Commissioner Gopal Baglay and his team in securing the release," External Affairs Minister S Jaishankar said in a tweet.
Both Sri Lankan officials and the Indian diplomatic sources confirmed the release and noted that with Tuesday's release there are no more Indian fishermen in the island nation's custody.
The court order for the release of fishermen came as the Indian authorities urged Sri Lanka to release them on humanitarian grounds in the backdrop of economic assistance talks that were going on at the time.
India this month announced an economic relief package to Sri Lanka to help its southern neighbour tackle its worst foreign exchange crisis.
The issue of fishermen had figured in the talks between Finance Minister Basil Rajapaksa and External Affairs Minister Jaishankar early this month.
Last month, India had expressed concern over the detention of 68 of its fishermen from Tamil Nadu by Sri Lankan authorities and said the issue of their "early release" has been taken up with the island nation.
The issue of fishermen remains one of the irritants in India and Sri Lanka ties.
There have been several alleged incidents of Sri Lankan Navy personnel even firing at Indian fishermen in the Palk Strait and seizing their boats.
The Palk Strait, which is a narrow strip of water separating Tamil Nadu from Sri Lanka, is a rich fishing ground for fishermen from both countries.
The release of fishermen comes on a day when Tamil Nadu Chief Minister MK Stalin urged the Centre to take up the issue with the Sri Lankan government in a stern manner and also register its disapproval over the island nation's decision to auction boats seized from the Indian fishermen.
In a letter addressed to Prime Minister Narendra Modi, Stalin exhorted the Centre to register its disapproval in the "strongest possible terms at the appropriate level" and also prevail upon the Lankan government to recall the advertisement for auctioning Tamil Nadu fishing boats on which they do not have any legal rights.
In the letter to PM Modi, Mr Stalin said steps should be taken to ensure the early release of 75 boats and fishing gear seized after 2018 by the Sri Lankan navy.
He expressed "a deep sense of disappointment" over the move to auction 105 fishing boats belonging to Tamil Nadu fishermen that are in the custody of Sri Lankan authorities.
Mr Stalin said India cannot continue to be seen as a mute spectator as the rights of Indian fishermen are repeatedly trampled upon.
He requested the government of India to take this up with the Sri Lankan government in a "stern manner such that acts of physical assault and robbing or damaging of assets of fishermen does not take place in future."
(Except for the headline, this story, originally published by PTI has not been edited by SLM staff)